This release is a pre-release and may not be stable for production use.
NanoEpiSeg 1.0.0b3
NanoEpiSeg is a tool for de novo segmentation of a methylome from read-level methylation calls (such as Nanopolish).
NanoEpiSeg is currently in development. Please do not hesitate to report bugs or feature requests.
A detailed documentation is in the works, stay tuned!
Prerequisites
NanoEpiSeg assumes that your methylation calls are stored in MetH5 format.
Installation
Through pip:
pip install nanoepiseg
Through anaconda:
conda install -c snajder-r nanoepiseg
Usage
NanoEpiSeg is meant to be parallelizable, which is why you would typically call nanoepiseg on a cluster system in parallel. In order to best accomplish load-balancing, it is done per hdf5 chunk.
You can list the number of chunks per chromosome via:
nanoepiseg list_chunks --m5file INPUT_FILE.m5
To then perform segmentation for a certain chunk, you can run:
nanoepiseg segment_h5 --m5file INPUT_FILE.m5 \
--out_tsv OUTPUT_FILE \
--reader_workers NUM_READER_WORKERS \
--workers NUM_SEGMENTATION_WORKERS \
--chromosome CHROMOSOME \
--chunks CHUNK1 [CHUNK2 ...]
There are further options available. Please check out the help to discover them.
1 maintainer
Metadata
1 maintainer
Release files for nanoepiseg 1.0.0b3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| nanoepiseg-1.0.0b3.tar.gz | 14.3 kB | Without provenance | Details for nanoepiseg-1.0.0b3.tar.gz |
Release files / nanoepiseg-1.0.0b3.tar.gz
| Download URL | nanoepiseg-1.0.0b3.tar.gz |
|---|---|
| Size | 14.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
5903ae1962fa6641f56000b935c95897d7ae75cd039ed352e2cb376a8bc8f414
|
|
BLAKE2b-256 checksum How to use checksums |
3bbc9402364807da2cd28fd4bf26738cf61739cf81aad9fad3b7ddbb07f87879
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/4.0.1 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.60.0 CPython/3.7.0
|
Security for nanoepiseg 1.0.0b3
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
